Update to ruff 0.16.x, make required fixes

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ ci:
   submodules: false
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.22 # Ruff version
+    rev: v0.16.6 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

examples/grits.ipynb

@@ -21,8 +21,7 @@
    "source": [
     "import mbuild as mb\n",
     "\n",
-    "from grits import backmap\n",
-    "from grits import CG_Compound"
+    "from grits import CG_Compound, backmap"
    ]
   },
   {

grits/__init__.py

@@ -13,10 +13,10 @@
     pass
 
 __all__ = [
-    "__version__",
+    "Bead",
     "CG_Compound",
     "CG_System",
-    "Bead",
+    "__version__",
     "backmap",
     "utils",
 ]

grits/coarsegrain.py

@@ -29,7 +29,7 @@
     has_number,
 )
 
-__all__ = ["CG_Compound", "CG_System", "Bead"]
+__all__ = ["Bead", "CG_Compound", "CG_System"]
 
 
 class CG_Compound(Compound):
@@ -101,7 +101,7 @@ def __init__(
         aniso_beads=False,
         **kwargs,
     ):
-        super(CG_Compound, self).__init__(**kwargs)
+        super().__init__(**kwargs)
         if (beads is None) == (mapping is None):
             raise ValueError(
                 "Please provide only one of either beads or mapping."
@@ -120,7 +120,7 @@ def __init__(
                 # to be set correctly.
                 with tempfile.NamedTemporaryFile() as f:
                     mol.write(format="mol2", filename=f.name, overwrite=True)
-                    mol = list(pybel.readfile("mol2", f.name))[0]
+                    mol = next(iter(pybel.readfile("mol2", f.name)))
 
                 mol.OBMol.AddHydrogens()  # mol.addh()
                 n_atoms2 = mol.OBMol.NumAtoms()
@@ -294,7 +294,11 @@ def save_mapping(self, filename=None):
         return filename
 
     def visualize(
-        self, show_ports=False, color_scheme={}, show_atomistic=False, scale=1.0
+        self,
+        show_ports=False,
+        color_scheme=None,
+        show_atomistic=False,
+        scale=1.0,
     ):  # pragma: no cover
         """Visualize the Compound using py3dmol.
 
@@ -322,6 +326,8 @@ def visualize(
         -------
         view : py3Dmol.view
         """
+        if color_scheme is None:
+            color_scheme = {}
         if not run_from_ipython():
             raise RuntimeError(
                 "Visualization is only supported in Jupyter Notebooks."
@@ -455,7 +461,7 @@ class Bead(Compound):
     def __init__(self, smarts=None, orientation=None, **kwargs):
         self.smarts = smarts
         self.orientation = orientation
-        super(Bead, self).__init__(element=None, **kwargs)
+        super().__init__(element=None, **kwargs)
 
 
 class CG_System:
@@ -752,7 +758,7 @@ def save(self, cg_gsdfile, start=0, stop=None, stride=1):
                             heavy_positions = positions[
                                 np.where(masses > hmass)
                             ]
-                            major_axis, ab_idxs = get_major_axis(
+                            major_axis, _ab_idxs = get_major_axis(
                                 heavy_positions
                             )
                             orientation.append(get_quaternion(major_axis))

grits/finegrain.py

@@ -29,12 +29,12 @@ def fg_particles():
         """Set the particles of the fine-grained structure."""
         fine_grained = Compound()
 
-        anchors = dict()
+        anchors = {}
         for i, bead in enumerate(cg_compound):
             smiles = bead.smarts
             b = load(smiles, smiles=True)
             b.translate_to(bead.pos)
-            anchors[i] = dict()
+            anchors[i] = {}
             if cg_compound.anchors is not None:
                 for index in cg_compound.anchors[bead.name]:
                     anchors[i][index] = b[index]
@@ -45,7 +45,7 @@ def fg_bonds():
         """Set the bonds for the fine-grained structure."""
         bonded_atoms = []
         remove_hs = []
-        rotated = {k: False for k in anchors.keys()}
+        rotated = {k: False for k in anchors}
         for name, inds in cg_compound.bond_map:
             for ibead, jbead in cg_compound.bonds():
                 names = [ibead.name, jbead.name]
@@ -61,12 +61,12 @@ def fg_bonds():
                 try:
                     iatom = anchors[i].pop(fi)
                 except KeyError:
-                    fi = [x for x in inds if x in anchors[i]][0]
+                    fi = next(x for x in inds if x in anchors[i])
                     iatom = anchors[i].pop(fi)
                 try:
                     jatom = anchors[j].pop(fj)
                 except KeyError:
-                    fj = [x for x in inds if x in anchors[j]][0]
+                    fj = next(x for x in inds if x in anchors[j])
                     jatom = anchors[j].pop(fj)
 
                 hi = get_hydrogen(fine_grained, iatom)

grits/tests/test_coarsegrain.py

@@ -25,7 +25,7 @@ def test_initmethane(self, methane):
         assert cg_methane.n_particles == 1
         assert isinstance(cg_methane, CG_Compound)
 
-        types = set([i.name for i in cg_methane.particles()])
+        types = {i.name for i in cg_methane.particles()}
         assert "_A" in types
         assert len(types) == 1
         assert np.isclose(cg_methane.mass, 16.043, atol=1e-5)
@@ -38,7 +38,7 @@ def test_initanisomethane(self, methane):
         assert cg_methane.n_particles == 1
         assert isinstance(cg_methane, CG_Compound)
 
-        types = set([i.name for i in cg_methane.particles()])
+        types = {i.name for i in cg_methane.particles()}
         assert "_A" in types
         assert len(types) == 1
         assert np.isclose(cg_methane.mass, 16.043, atol=1e-5)
@@ -54,7 +54,7 @@ def test_initp3ht(self, p3ht):
         assert cg_p3ht.n_particles == 48
         assert isinstance(cg_p3ht, CG_Compound)
 
-        types = set([i.name for i in cg_p3ht.particles()])
+        types = {i.name for i in cg_p3ht.particles()}
         assert "_B" in types
         assert "_S" in types
         assert len(types) == 2
@@ -69,7 +69,7 @@ def test_initanisop3ht(self, p3ht):
         assert cg_p3ht.n_particles == 48
         assert isinstance(cg_p3ht, CG_Compound)
 
-        types = set([i.name for i in cg_p3ht.particles()])
+        types = {i.name for i in cg_p3ht.particles()}
         assert "_B" in types
         assert "_S" in types
         assert len(types) == 2
@@ -87,7 +87,7 @@ def test_initp3htoverlap(self, p3ht):
         assert cg_p3ht.n_particles == 48
         assert isinstance(cg_p3ht, CG_Compound)
 
-        types = set([i.name for i in cg_p3ht.particles()])
+        types = {i.name for i in cg_p3ht.particles()}
         assert "_B" in types
         assert "_S" in types
         assert len(types) == 2
@@ -102,7 +102,7 @@ def test_initanisop3htoverlap(self, p3ht):
         assert cg_p3ht.n_particles == 48
         assert isinstance(cg_p3ht, CG_Compound)
 
-        types = set([i.name for i in cg_p3ht.particles()])
+        types = {i.name for i in cg_p3ht.particles()}
         assert "_B" in types
         assert "_S" in types
         assert len(types) == 2
@@ -115,7 +115,7 @@ def test_initmapp3ht(self, p3ht, p3ht_mapping):
         assert cg_p3ht.n_particles == 48
         assert isinstance(cg_p3ht, CG_Compound)
 
-        types = set([i.name for i in cg_p3ht.particles()])
+        types = {i.name for i in cg_p3ht.particles()}
         assert "_B" in types
         assert "_S" in types
         assert len(types) == 2
@@ -126,7 +126,7 @@ def test_initmapanisop3ht(self, p3ht, p3ht_mapping):
         assert cg_p3ht.n_particles == 48
         assert isinstance(cg_p3ht, CG_Compound)
 
-        types = set([i.name for i in cg_p3ht.particles()])
+        types = {i.name for i in cg_p3ht.particles()}
         assert "_B" in types
         assert "_S" in types
         assert len(types) == 2
@@ -139,7 +139,7 @@ def test_initmapmethane(self, methane, methane_mapping):
         assert cg_methane.n_particles == 1
         assert isinstance(cg_methane, CG_Compound)
 
-        types = set([i.name for i in cg_methane.particles()])
+        types = {i.name for i in cg_methane.particles()}
         assert "_A" in types
         assert len(types) == 1
 
@@ -151,7 +151,7 @@ def test_initmapanisomethane(self, methane, methane_mapping):
         assert cg_methane.n_particles == 1
         assert isinstance(cg_methane, CG_Compound)
 
-        types = set([i.name for i in cg_methane.particles()])
+        types = {i.name for i in cg_methane.particles()}
         assert "_A" in types
         assert len(types) == 1
         for particle in cg_methane.particles():

grits/utils.py

@@ -23,7 +23,7 @@ def default(self, obj):
         elif isinstance(obj, np.ndarray):
             return obj.tolist()
         else:
-            return super(NumpyEncoder, self).default(obj)
+            return super().default(obj)
 
 
 def comp_from_snapshot(snapshot, indices, length_scale=1.0, mass_scale=1.0):
@@ -284,7 +284,7 @@ def get_com(particle_positions, particle_masses):
     return center_of_mass
 
 
-def get_quaternion(n1, n0=np.array([0, 0, 1])):
+def get_quaternion(n1, n0=(0, 0, 1)):
     """Calculate rotation quaternion from axis vectors.
 
     Calculate axis and angle of rotation given
@@ -295,7 +295,7 @@ def get_quaternion(n1, n0=np.array([0, 0, 1])):
     ----------
         n1 : numpy array
             numpy array that is the major axis vector.
-        n0 : numpy array
+        n0 : numpy array, default (0,0,1)
             numpy array that is used to define the default quaternion.
             Defaults to the Z-axis.
 
@@ -305,12 +305,15 @@ def get_quaternion(n1, n0=np.array([0, 0, 1])):
             numpy array that tells the position of the monomer in units
             of a quaternion.
     """
+    n0 = np.asarray(n0)
     if n1 is None:  # one atom in this bead -> default quaternion
         warnings.warn(
             "get_quaternion was called with None as input!\n\
                       Returning default orientation."
         )
         return np.array([0, 0, 0, 1])
+    else:
+        n1 = np.asarray(n1)
     V_axis = np.cross(n0, n1)
     theta_numerator = np.dot(n0, n1)
     theta_denominator = np.linalg.norm(n0) * np.linalg.norm(n1)